User:Loïc Gazquez/Sandbox 24

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Active site
The firefly luciferase interacts with ATP, luciferin, an Acetyl-coenzyme A (CoA ) and O2. So differents groups of residues are part of the the ligand binding. Those residues can be placed in the molecule by comparing the sequence of different enzymes of the same family. The ATP binds to a G-x-x-x-x-G-K-[STG] sequence which is a very disordered version of a classical mononucleotide-binding motif. The luciferin-binding site seems to be a depression between β sheet B and the barrel subdomain, but is not clearly visible on the structure. The CoA-binding site does not have a classical motif of adenylate forming enzyme and this luciferase is the first member of a new superfamily to be studied. The adenylate forming reaction is likely to involve a few glycine or charged residues. The others binding sites are not clearly defined yet but there are some conserved residues taking part in the binding or the catalysis:


 * Thr346 which is the only residue with dihedral angles outside of the usual regions of the Ramachandran plot. This energetically unfavorable angles are usually in relation with residues having important functional roles.


 * Asp422 is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the Tyr340.


 * Ser420 has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.

All the conserved residues are either on the surface of the two domains on the side of the cleft or on the loop connecting the two domains. But this cleft is too big to accomodate on the substrates and is seems that the two domains only come closer around the products when they are formed.